Files structure

[eluser]adamfairholm[/eluser]
I'd try modules (such as Modular Extensions) to keep your application files in modules and nice and separated:

https://bitbucket.org/wiredesignz/codeigniter-modular-extensions-hmvc/overview

If you want to organize files other than controllers and views, check out packages as well:

http://ellislab.com/codeigniter/user-gui...oader.html